Organism : Bacillus subtilis | Module List :
VIMSS39865

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VIMSS39865
(Mouseover regulator name to see its description)

VIMSS39865 is regulated by 32 influences and regulates 0 modules.
Regulators for VIMSS39865 (32)
Regulator Module Operator
BSU00230 158 tf
BSU00800 158 tf
BSU01810 158 tf
BSU02550 158 tf
BSU03960 158 tf
BSU04060 158 tf
BSU05130 158 tf
BSU11500 158 tf
BSU13210 158 tf
BSU15330 158 tf
BSU15690 158 tf
BSU16600 158 tf
BSU18460 158 tf
BSU23100 158 tf
BSU29000 158 tf
BSU29740 158 tf
BSU34220 158 tf
BSU35520 158 tf
BSU36020 158 tf
BSU36420 158 tf
BSU38910 158 tf
BSU40010 158 tf
BSU01010 287 tf
BSU01640 287 tf
BSU01810 287 tf
BSU02680 287 tf
BSU09330 287 tf
BSU10860 287 tf
BSU16600 287 tf
BSU24320 287 tf
BSU37160 287 tf
BSU38600 287 tf

Warning: VIMSS39865 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5264 7.10e-18 AGGGTGGTACCgCGg
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5265 4.60e-05 tctCgtCCCT
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5512 4.90e-05 AAGGaGaG
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5513 2.20e+02 CATAaa.TagaaaGagGTgTta
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for VIMSS39865

Warning: No Functional annotations were found!

Module neighborhood information for VIMSS39865

VIMSS39865 has total of 44 gene neighbors in modules 158, 287
Gene neighbors (44)
Gene Common Name Description Module membership
BSU02090 ybxI exported beta-lactamase (RefSeq) 171, 287
BSU05220 ydeJ putative lipoprotein (RefSeq) 171, 287
BSU07440 yfmK putative acetyltransferase (RefSeq) 171, 287
BSU10300 aprE serine alkaline protease (subtilisin E) (RefSeq) 114, 287
BSU11420 trpS tryptophanyl-tRNA synthetase (RefSeq) 42, 158
BSU13120 proB gamma-glutamyl kinase (RefSeq) 42, 158
BSU13130 proA gamma-glutamyl phosphate reductase (RefSeq) 42, 158
BSU13940 ykwB putative acetyltransferase (RefSeq) 171, 287
BSU15430 ileS isoleucyl-tRNA synthetase (RefSeq) 158, 300
BSU18350 dacC D-alanyl-D-alanine carboxypeptidase (RefSeq) 136, 287
BSU18360 yoxA putative epimerase (RefSeq) 136, 287
BSU18370 yoeA putative efflux transporter (RefSeq) 171, 287
BSU26370 yqaC hypothetical protein (RefSeq) 171, 287
BSU27410 alaS alanyl-tRNA synthetase (RefSeq) 79, 158
BSU27560 hisS histidyl-tRNA synthetase (RefSeq) 158, 300
BSU28420 ysmA hypothetical protein (RefSeq) 171, 287
BSU28630 pheT phenylalanyl-tRNA synthetase subunit beta (RefSeq) 158, 343
BSU28640 pheS phenylalanyl-tRNA synthetase subunit alpha (RefSeq) 158, 343
BSU30320 leuS leucyl-tRNA synthetase (RefSeq) 158, 300
BSU30360 yttA hypothetical protein (RefSeq) 171, 287
BSU31945 BSU31945 None 69, 287
BSU38470 ywaD double-zinc aminopeptidase (RefSeq) 101, 287
BSU39110 deaD ATP-dependent RNA helicase (RefSeq) 125, 158
BSU39120 yxiM putative esterase (lipoprotein) (RefSeq) 125, 158
BSU39140 yxiK putative phage head maturation protein (RefSeq) 125, 158
BSU39150 yxiJ hypothetical protein (RefSeq) 125, 158
BSU39160 yxiI hypothetical protein (RefSeq) 125, 158
BSU39170 yxzG putative nucleic acid binding protein (RefSeq) 125, 158
BSU39180 yxiH hypothetical protein (RefSeq) 125, 158
BSU39190 yxiG hypothetical protein (RefSeq) 125, 158
BSU39200 yxzC putative nucleic acid binding protein (RefSeq) 125, 158
BSU39210 yxiF putative phage reverse transcriptase or polymerase (RefSeq) 125, 158
BSU39220 yxxG hypothetical protein (RefSeq) 125, 158
BSU39230 wapA cell wall-associated protein precursor (RefSeq) 125, 158
BSU40022 BSU40022 None 117, 287
BSU40250 yycR putative dehydrogenase (RefSeq) 136, 287
BSU40290 yycN putative N-acetyltransferase (RefSeq) 114, 287
BSU40300 rapG response regulator aspartate phosphatase (RefSeq) 101, 287
BSU40630 yybI inner spore coat protein (RefSeq) 114, 287
BSU40640 yybH hypothetical protein (RefSeq) 171, 287
VIMSS37404 VIMSS37404 None 70, 287
VIMSS38706 VIMSS38706 None 117, 287
VIMSS39865 VIMSS39865 None 158, 287
VIMSS40339 VIMSS40339 None 70, 287
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for VIMSS39865
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend